A motor control system of an electric vehicle, a controlling method for the motor control system and an electric vehicle are provided. The motor control system includes: an IGBT module, connected with a motor of the electric vehicle; a detection module, configured to detect a motor speed; a drive module, configured to drive IGBTs in the IGBT module to turn on or off so as to control the motor to work or stop working; a first control module; a second control module communicated with the first control module; and a channel selection module, configured to select a channel of the second control module when the first control module has a fault. When the second control module is selected, it sends a second control signal to the drive module according to the motor speed at a predetermined time before the first control module has the fault, so as to control the motor to stop working.